I really don't find it strange that a seiyū would play a protagonist in one series and a antagonist in another. They are actors, it's their job to be able play lots of different kind of roles. So for me it's more like if I start watching a new series and hear a familiar voice I'll look to see who the seiyū is and what other roles they've played. However there haven't been to many times I've been like, "Wow, I can't believe they also voice __!"

So,these are the ones I can think of off the top of my head:
Kamiya Hiroshi who plays Orihara Izaya (Drrr!!) but I was very surprised to find he also plays Mephisto Pheles (Ao no Exorcist)
He's one of my favorite seiyū and I had no idea until half way through Ao no Exorcist that it was him!

Also, Nakamura Yūichi who plays Greed (FMA: Brotherhood), Gray Fullbuster (Fairy Tail), Kyohei Kadota (Drrr!!), Sakata Kintoki (Gintama) and many many more! He's the one that does surprise me on a regular basis.

Aoi Yuuki - She did, at the same time, Victorique in Gosick and Madoka in Puella Magi Madoka Magica. The two characters are entirely different in almost every way. Other rolls she has done: Noel in So Ra No Wo To; Alice in Croisee in a Foreign Labyrinth; and Tooru in A Channel.

Kikuko Inoue - The voice of Belldandy in Ah! My Goddess! The personification of Yamato Nadeshiko, she also specializes in roles like "Hot Shounen Mom" and "Onee-sama". However, in Otome Youkai Zakuro, she played the villain: Rangui! That is range! (Oh, and she's 17 years old. ALWAYS )

She is the Japanese voice actress of Usagi Tsukino from Sailor Moon, Excel Excel from Excel Saga, Birdy Cephon Altera from Birdy the Mighty (The original OVAs from 1996, not the newer 2008 series Birdy the Mighty: Decode), Koume Sawaguchi from Blue Seed, Urumi Kanzaki from Great Teacher Onizuka and Misato Katsuragi from Neon Genesis Evangelion.

It's not that I'd didn't expect her to be the voices, it's just the range and talent she has for what she loves doing is really something.

I have a pretty good ear when recognizing voices of the seiyuu , I have listened to a lot of voice actors in the past 8 years and picking up on their cadence in their speech patterns.
Its part of my other job...listening to speech

.There are voice actors who has a wider range of characters than others and can do a pretty job at it and one of the seiyuu I have been watching for a long time and who falls in that category is Fukuyama Jun.

I really love his later character in Ixion Saga DT as the crossdressing transgender Marian.

Daisuke Ono as the flower shop keeper in Tamako Market was a surprise to me too. He was famous for his role as Seabstian but I like him more as Shizuo in Durarara.

Also Morikawa Toshiyuki as Mama Panda was a surprise too. I could not recognize his voice there. And I have heard him in so many roles already and met and talked with him but I could not pick it up the voice but I was able to recognize his speech pattern .